I need certain customizations in the UML diagrams so I've decided to get
the source code, change what I need in the models, regenerate generator
model and then regenerate diagram's code (Using Generate UML2tools
Diagrams)

Well, I can regenerate the gmfGen model (ignoring validation errors as
I've read I must do) and then the code. However, in the generated class
UMLElementTypes.java, the type's ids are changed and those changes in the
ids are not propagated across the rest of the generated code. I would
expect such behavior in those parts tagged with @generated NOT but no in
the re-generated classes, and methods.
Then, after de generation, I Have many classes referencing non-existing
UMLElementTypes.

¿I'm missing something? Maybe the problem come from the GMF generator ¿Do
you need a specific version of GMF to generate the code?